PRINCIPLES OF BIOCHEMISTRY Chapter 15 Principles of Metabolic Regulation

15.1 Regulation of Metabolic Pathways 15.2 Analysis of Metabolic Control 15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis 15.4 The Metabolism of Glycogen in Animals 15.5 Coordinated Regulation of Glycogen Synthesis and Breakdown p.569

Every pathway we discuss in this book is inextricably intertwined with all the other cellular pathways in a multidimensional network of reactions (Fig. 15–1). p.569

FIGURE 15-1 FIGURE 15–1 Metabolism as a three-dimensional meshwork. p.570

15.1 Regulation of Metabolic Pathways Cells and Organisms Maintain a Dynamic Steady State Fuels such as glucose enter a cell, and waste products such as CO2 leave, but the mass and the gross composition of a typical cell, organ, or adult animal do not change appreciably over time; cells and organisms exist in a dynamic steady state. Although the rate (v) of metabolite flow, or flux, through this step of the pathway may be high and variable, the concentration of substrate, S, remains constant. So, for the two-step reaction p.570

when v1 = v2, [S] is constant. A → S → P when v1 = v2, [S] is constant. This is homeostasis at the molecular level. Both the Amount and the Catalytic Activity of an Enzyme Can Be Regulated Extracellular signals (Fig. 15–2, ) may be hormonal (insulin or epinephrine, for example) or neuronal (acetylcholine), or may be growth factors or cytokines. p.571

Transcription factors are nuclear proteins that, when activated, bind specific DNA regions (response elements) near a gene’s promoter (its transcriptional starting point) and activate or repress the transcription of that gene, leading to increased or decreased synthesis of the encoded protein. Rapid turnover is energetically expensive, but proteins with a short half-life can reach new steady state levels much faster than those with a long half-life, and the benefit of this quick responsiveness must balance or outweigh the cost to the cell. p.571

FIGURE 15-2 FIGURE 15–2 Factors affecting the activity of enzymes. p.572

These global changes in gene expression can be quantified by the use of DNA microarrays that display the entire complement of mRNAs present in a given cell type or organ (the transcriptome) or by twodimensional gel electrophoresis that displays the protein complement of a cell type or organ (its proteome). The effect of changes in the proteome is often a change in the total ensemble of low molecular weight metabolites, the metabolome. p.572

Covalent modifications of enzymes or other proteins (Fig Covalent modifications of enzymes or other proteins (Fig. 15–2, ) occur within seconds or minutes of a regulatory signal, typically an extracellular signal. By far the most common modifications are phosphorylation and dephosphorylation (Fig. 15–3); up to half the proteins in a eukaryotic cell are phosphorylated under some circumstances. p.573

FIGURE 15-3 FIGURE 15–3 Protein phosphorylation and dephosphorylation.

Metabolic regulation refers to processes that serve to maintain homeostasis at the molecular level—to hold some cellular parameter at a steady level over time. The term metabolic control refers to a process that leads to a change in the output of a metabolic pathway over time, in response to some outside signal or change in circumstances. p.574

Reactions Far from Equilibrium in Cells Are Common Points of Regulation For some steps in a metabolic pathway the reaction is close to equilibrium, with the cell in its dynamic steady state (Fig. 15–4). these near-equilibrium reactions in a cell by comparing the mass action ratio, Q, with the equilibrium constant for the reaction, Keq. Recall that for the reaction A + B → C + D, Q = [C][D]/[A][B]. p.574

FIGURE 15-4 FIGURE 15–4 Near-equilibrium and nonequilibrium steps in a metabolic pathway. p.574

Adenine Nucleotides Play Special Roles in Metabolic Regulation After the protection of its DNA from damage, perhaps nothing is more important to a cell than maintaining a constant supply and concentration of ATP. If [ATP] were to drop significantly, these enzymes would be less than fully saturated by their substrate (ATP), and the rates of hundreds of reactions that involve ATP would decrease (Fig. 15–5). p.575

FIGURE 15-5 FIGURE 15–5 Effect of ATP concentration on the initial velocity of a typical ATP-dependent enzyme. p.575

ATP + glucose ─→ ADP + glucose 6-phosphate There is also an important thermodynamic effect of lowered [ATP]. ATP + glucose ─→ ADP + glucose 6-phosphate Note that this expression holds true only when reactants and products are at their equilibrium concentrations, where ΔG' = 0. p.575

The most important mediator of regulation by AMP is AMP-activated protein kinase (AMPK), which responds to an increase in [AMP] by phosphorylating key proteins and thus regulating their activities. p.576

FIGURE 15–6 FIGURE 15–6 Role of AMP-activated protein kinase (AMPK) in carbohydrate and fat metabolism. p.576

15.2 Analysis of Metabolic Control The Contribution of Each Enzyme to Flux through a Pathway Is Experimentally Measurable There are several ways to determine experimentally how a change in the activity of one enzyme in a pathway affects metabolite flux through that pathway. Consider the experimental results shown in Figure 15–7. p.577

FIGURE 15-7 FIGURE 15–7 Dependence of glycolytic flux in a rat liver homogenate on added enzymes. p.578

The Control Coefficient Quantifies the Effect of a Change in Enzyme Activity on Metabolite Flux through a Pathway Quantitative data on metabolic flux, obtained as described in Figure 15–7, can be used to calculate a flux control coefficient, C, for each enzyme in a pathway. p.578

FIGURE 15-8 FIGURE 15–8 Flux control coefficient, C, in a branched metabolic pathway. p.537

The Elasticity Coefficient Is Related to an Enzyme’s Responsiveness to Changes in Metabolite or Regulator Concentrations A second parameter, the elasticity coefficient, ε, expresses quantitatively the responsiveness of a single enzyme to changes in the concentration of a metabolite or regulator; it is a function of the enzyme’s intrinsic kinetic properties. For example, an enzyme with typical Michaelis-Menten kinetics shows a hyperbolic response to increasing substrate concentration (Fig. 15–9). p.580

FIGURE 15–9 FIGURE 15–9 Elasticity coefficient, ε, of an enzyme with typical Michaelis-Menten kinetics. p.580

The Response Coefficient Expresses the Effect of an Outside Controller on Flux through a Pathway The experiment would measure the flux through the pathway (glycolysis, in this case) at various levels of the parameter P (the insulin concentration, for example) to obtain the response coefficient, R, which expresses the change in pathway flux when P ([insulin]) changes. The three coefficients C, ε, and R are related in a simple way: R = C．ε p.581

Metabolic Control Analysis Has Been Applied to Carbohydrate Metabolism, with Surprising Results Metabolic control analysis provides a framework within which we can think quantitatively about regulation, interpret the significance of the regulatory properties of each enzyme in a pathway, identify the steps that most affect the flux through the pathway, and distinguish between regulatory mechanisms that act to maintain metabolite concentrations and control mechanisms that actually alter the flux through the pathway. p.581

Investigators have used nuclear magnetic resonance (NMR) as a noninvasive means to determine the concentration of glycogen and metabolites in the five-step pathway from glucose in the blood to glycogen in myocytes (Fig. 15–10) in rat and human muscle. p.581

FIGURE 15-10 FIGURE 15–10 Control of glycogen synthesis from blood glucose in muscle. p.581

Metabolic Control Analysis Suggests a General Method for Increasing Flux through a Pathway Metabolic control analysis predicts, and experiments have confirmed, that flux toward a specific product is most effectively increased by raising the concentration of all enzymes in the pathway. p.582

15.3 Coordinated Regulation of Glycolysis and Gluconeogenesis Seven of the glycolytic reactions are freely reversible, and the enzymes that catalyze these reactions also function in gluconeogenesis (Fig. 15–11). This uneconomical process has been called a futile cycle. Such cycles may provide advantages for controlling pathways, and the term substrate cycle is a better description. p.582

FIGURE 15-11 FIGURE 15–11 Glycolysis and gluconeogenesis. p.583

Hexokinase Isozymes of Muscle and Liver Are Affected Differently by Their Product, Glucose 6-Phosphate The predominant hexokinase isozyme of myocytes (hexokinase II) has a high affinity for glucose. Muscle hexokinase I and hexokinase II are allosterically inhibited by their product, glucose 6-phosphate. The predominant hexokinase isozyme of liver is hexokinase IV (glucokinase), which differs in three important respects from hexokinases I–III of muscle. p.583

FIGURE 15-12 FIGURE 15–12 Comparison of the kinetic properties of hexokinase IV (glucokinase) and hexokinase I. p.585

FIGURE 15-13 FIGURE 15–13 Regulation of hexokinase IV (glucokinase) by sequestration in the nucleus. p.585

Phosphofructokinase-1 and Fructose 1,6-bisphosphatase Are Reciprocally Regulated ATP is not only a substrate for PFK-1 but also an end product of the glycolytic pathway. When high cellular [ATP] signals that ATP is being produced faster than it is being consumed, ATP inhibits PFK-1 by binding to an allosteric site and lowering the affinity of the enzyme for its substrate fructose 6-phosphate (Fig. 15–14). The corresponding step in gluconeogenesis is the conversion of fructose 1,6-bisphosphate to fructose 6- phosphate (Fig. 15–15). p.586

FIGURE 15-14(a) FIGURE 15–14 Phosphofructokinase-1 (PFK-1) and its regulation. p.586

FIGURE 15-14(b) p.586

FIGURE 15-14(c) p.586

FIGURE 15-15 FIGURE 15–15 Regulation of fructose 1,6-bisphosphatase (FBPase-1) and phosphofructokinase-1 (PFK-1). p.586

Fructose 2,6-Bisphosphate Is a Potent Allosteric Regulator of PFK-1 and FBPase-1 When the blood glucose level decreases, the hormone glucagon signals the liver to produce and release more glucose and to stop consuming it for its own needs. The rapid hormonal regulation of glycolysis and gluconeogenesis is mediated by fructose 2,6- bisphosphate, an allosteric effector for the enzymes PFK-1 and FBPase-1: p.587

When fructose 2,6-bisphosphate binds to its allosteric site on PFK-1, it increases the enzyme’s affinity for its substrate fructose 6-phosphate and reduces its affinity for the allosteric inhibitors ATP and citrate (Fig. 15–16). p.587

FIGURE 15-16(a) FIGURE 15–16 Role of fructose 2,6-bisphosphate in regulation of glycolysis and gluconeogenesis. p.587

FIGURE 15-16(b) p.587

FIGURE 15-16(c) p.587

The cellular concentration of the allosteric regulator fructose 2,6-bisphosphate is set by the relative rates of its formation and breakdown (Fig. 15–17a). It is formed by phosphorylation of fructose 6-phosphate, catalyzed by phosphofructokinase-2 (PFK-2), and is broken down by fructose 2,6-bisphosphatase (FBPase- 2). p.588

FIGURE 15-17(a) FIGURE 15–17 Regulation of fructose 2,6-bisphosphate level. p.588

FIGURE 15-17(b) p.588

Xylulose 5-Phosphate Is a Key Regulator of Carbohydrate and Fat Metabolism The xylulose 5-phosphate concentration rises as glucose entering the liver is converted to glucose 6-phosphate and enters both the glycolytic and pentose phosphate pathways. Xylulose 5-phosphate activates phosphoprotein phosphatase 2A (PP2A; Fig. 15–18), which dephosphorylates the bifunctional PFK-2/FBPase-2 enzyme. p.588

FIGURE 15-18(a) FIGURE 15–18 Structure and action of phosphoprotein phosphatase 2A (PP2A). p.589

FIGURE 15-18(b) p.589

The Glycolytic Enzyme Pyruvate Kinase Is Allosterically Inhibited by ATP High concentrations of ATP, acetyl-CoA, and long-chain fatty acids (signs of abundant energy supply) allosterically inhibit all isozymes of pyruvate kinase (Fig. 15–19). p.589

FIGURE 15-19 FIGURE 15–19 Regulation of pyruvate kinase. p.589

The Gluconeogenic Conversion of Pyruvate to Phosphoenol Pyruvate Is Under Multiple Types of Regulation In the pathway leading from pyruvate to glucose, the first control point determines the fate of pyruvate in the mitochondrion: its conversion either to acetyl-CoA (by the pyruvate dehydrogenase complex) to fuel the citric acid cycle (Chapter 16) or to oxaloacetate (by pyruvate carboxylase) to start the process of gluconeogenesis (Fig. 15–20). p.590

FIGURE 15-20 FIGURE 15–20 Two alternative fates for pyruvate. p.590

Transcriptional Regulation of Glycolysis and Gluconeogenesis Changes the Number of Enzyme Molecules One transcription factor important to carbohydrate metabolism is ChREBP (carbohydrate response element binding protein; Fig. 15–21), which is expressed primarily in liver, adipose tissue, and kidney. Another transcription factor in the liver, SREBP-1c, a member of the family of sterol response element binding proteins. p.591

TABLE 15-5 p.591

FIGURE 15-21 FIGURE 15–21 Mechanism of gene regulation by the transcription factor ChREBP. p.591

The transcription factor CREB (cyclic AMP response element binding protein) turns on the synthesis of glucose 6-phosphatase and PEP carboxykinase in response to the increase in [cAMP] triggered by glucagon. FOXO1 (forkhead box other) stimulates the synthesis of gluconeogenic enzymes and suppresses the synthesis of the enzymes of glycolysis, the pentose phosphate pathway, and triacylglycerol synthesis (Fig. 15–22). p.592

FIGURE 15-22 FIGURE 15–22 Mechanism of gene regulation by the transcription factor FOXO1. p.592

FIGURE 15-23 FIGURE 15–23 The PEP carboxykinase promoter region, showing the complexity of regulatory input to this gene. p.593

15.4 The Metabolism of Glycogen in Animals Glycogen, a storage form of carbohydrate, appears as electron-dense particles, often in aggregates or rosettes. In hepatocytes glycogen is closely associated with tubules of the smooth endoplasmic reticulum. Many mitochondria are also evident in this micrograph. Glycogen Breakdown Is Catalyzed by Glycogen Phosphorylase This process is repetitive; the enzyme removes successive glucose residues until it reaches the fourth glucose unit from a branch point (see Fig. 15–26). p.595

FIGURE 15-25 FIGURE 15–25 Removal of a glucose residue from the nonreducing end of a glycogen chain by glycogen phosphorylase. p.595

Glycogen phosphorylase acts repetitively on the nonreducing ends of glycogen branches until it reaches a point four glucose residues away from an (α1→6) branch point. Further degradation by glycogen phosphorylase can occur only after the debranching enzyme, formally known as oligo (α1→6) to (α1→4) glucan-transferase, catalyzes two successive reactions that transfer branches (Fig. 15– 26). p.596

FIGURE 15-26 FIGURE 15–26 Glycogen breakdown near an (1→6) branch point. p.596

Glucose 1-phosphate glucose 6-phosphate Glucose 1-Phosphate Can Enter Glycolysis or, in Liver, Replenish Blood Glucose Phosphoglucomutase: catalyzes the reversible reaction Glucose 1-phosphate glucose 6-phosphate Initially phosphorylated at a Ser residue, the enzyme donates a phosphoryl group to C-6 of the substrate, then accepts a phosphoryl group from C-1 (Fig. 15–27). p.596

The glucose 6-phosphate formed from glycogen in skeletal muscle can enter glycolysis and serve as an energy source to support muscle contraction. Glucose 6-phosphate formed in the cytosol is transported into the ER lumen by a specific transporter (T1) (Fig. 15– 28) and hydrolyzed at the lumenal surface by the glucose 6-phosphatase. p.596

The Sugar Nucleotide UDP-Glucose Donates Glucose for Glycogen Synthesis Many of the reactions in which hexoses are transformed or polymerized involve sugar nucleotides. The biological effect of branching is to make the glycogen molecule more soluble and to increase the number of nonreducing ends. p.596

FIGURE 15-27 FIGURE 15–27 Reaction catalyzed by phosphoglucomutase.

FIGURE 15-28 FIGURE 15–28 Hydrolysis of glucose 6-phosphate by glucose 6- phosphatase of the ER. p.597

FIGURE 15-29 FIGURE 15–29 Formation of a sugar nucleotide. p.600

FIGURE 15-30 FIGURE 15–30 Glycogen synthesis. p.600

FIGURE 15-31 FIGURE 15–31 Branch synthesis in glycogen. p.601

Glycogenin Primes the Initial Sugar Residues in Glycogen The intriguing protein glycogenin (Fig. 15–32) is both the primer on which new chains are assembled and the enzyme that catalyzes their assembly. The first step in the synthesis of a new glycogen molecule is the transfer of a glucose residue from UDP-glucose to the hydroxyl group of Tyr194 of glycogenin, catalyzed by the protein’s intrinsic glucosyltransferase activity (Fig. 15–33). p.601

FIGURE 15-32 FIGURE 15–32 Glycogenin structure. p.601

FIGURE 15-33(a) FIGURE 15–33 Glycogenin and the structure of the glycogen particle. p.602

FIGURE 15-33(b) p.602

15.5 Coordinated Regulation of Glycogen Synthesis and Breakdown Glycogen Phosphorylase Is Regulated Allosterically and Hormonally The glycogen phosphorylase of skeletal muscle exists in two interconvertible forms: glycogen phosphorylase a, and glycogen phosphorylase b. Enzyme cascade: a catalyst activates a catalyst, which activates a catalyst. The rise in [cAMP] activates cAMP-dependent protein kinase, also called protein kinase A (PKA). p.603

FIGURE 15-34 FIGURE 15–34 Regulation of muscle glycogen phosphorylase by covalent modification. p.603

PKA then phosphorylates and activates phosphorylase b kinase, which catalyzes the phosphorylation of Ser residues in each of the two identical subunits of glycogen phosphorylase, activating it and thus stimulating glycogen breakdown. When the muscle returns to rest, a second enzyme, phosphorylase a phosphatase, also called phosphoprotein phosphatase 1 (PP1), removes the phosphoryl groups from phosphorylase a, converting it to the less active form, phosphorylase b. p.603

FIGURE 15-35 FIGURE 15–35 Cascade mechanism of epinephrine and glucagon action. p.604

Glycogen Synthase Is Also Regulated by Phosphorylation and Dephosphorylation Like glycogen phosphorylase, glycogen synthase can exist in phosphorylated and dephosphorylated forms (Fig. 15–37). Its active form, glycogen synthase a, is unphosphorylated. The most important regulatory kinase is glycogen synthase kinase 3 (GSK3). p.605

FIGURGE 15-37 FIGURE 15–37 Effects of GSK3 on glycogen synthase activity. p.605

Glycogen Synthase Kinase 3 Mediates Some of the Actions of Insulin The action of GSK3 is hierarchical; it cannot phosphorylate glycogen synthase until another protein kinase, casein kinase II (CKII), has first phosphorylated the glycogen synthase on a nearby residue, an event called priming (Fig. 15–38a). Glycogen Synthase Kinase 3 Mediates Some of the Actions of Insulin One way in which insulin triggers intracellular changes is by activating a protein kinase (PKB) that in turn phosphorylates and inactivates GSK3. p.605

FIGURE 15-38(a) FIGURE 15–38 Priming of GSK3 phosphorylation of glycogen synthase. p.605

FIGURE 15-38(b) p.605

FIGURE 15-39 FIGURE 15–39 The path from insulin to GSK3 and glycogen synthase. p.606

Phosphoprotein Phosphatase 1 Is Central to Glycogen Metabolism Phosphoprotein phosphatase 1 does not exist free in the cytosol, but is tightly bound to its target proteins by one of a family of glycogen-targeting proteins that bind glycogen and each of the three enzymes, glycogen phosphorylase, phosphorylase kinase, and glycogen synthase. p.606

Allosteric and Hormonal Signals Coordinate Carbohydrate Metabolism Globally After ingestion of a carbohydrate-rich meal, the elevation of blood glucose triggers insulin release. p.606

FIGURE 15-40 FIGURE 15–40 Glycogen-targeting protein GM. p.607

FIGURE 15-41 FIGURE 15–41 Regulation of carbohydrate metabolism in the liver. p.607

The physiology of skeletal muscle differs from that of liver in three ways important to our discussion of metabolic regulation (Fig. 15–42): (1) muscle uses its stored glycogen only for its own needs; (2) as it goes from rest to vigorous contraction, muscle undergoes very large changes in its demand for ATP, which is supported by glycolysis; (3) muscle lacks the enzymatic machinery for gluconeogenesis. p.608

FIGURE 15-42 FIGURE 15–42 Difference in the regulation of carbohydrate metabolism in liver and muscle. p.608